molecular evolution Evidence and causes Simon Ho School of Biological Sciences Acknowledgements Rob Lanfear Lindell Bromham Matt Phillips Australian National University Julien ID: 552483
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Slide1
Time-dependent rates of molecular evolution Evidence and causes
Simon HoSchool of Biological SciencesSlide2
AcknowledgementsRob Lanfear, Lindell
Bromham, Matt PhillipsAustralian National UniversityJulien
Soubrier
, Alan CooperUniversity of AdelaideAllen RodrigoDuke University & University of AucklandJeremy and Barbara
2
AcknowledgementsSlide3
Morphological ratesMeasured in darwins or haldanesNeontological studiesPalaeontological studies
Differ by several orders of magnitude3
Introduction
Gingerich (2001)Slide4
Molecular rates: Pedigrees
4
Introduction
Howell
et al
. (2003)Slide5
Molecular rates: Phylogenies5
Introduction
0.06
difference
Rate
=
/ 6
Myr
=
0.01
/
Myr
6 MyrSlide6
Estimating rates6
Introduction
Fossil record
Biogeography
Sampling times
Pedigrees
A
B
A
B
Recent split
Fast rate
Ancient split
Slow rate
A
BSlide7
Calibration
7
IntroductionSlide8
Evidence8
Evidence
Birds (mtDNA)
Primates (mtDNA)
Primates (D-loop)
Ho
et al
. (2005)Slide9
Evidence9
Evidence
Genner
et al
. (2007)
Burridge
et al
. (2008)Slide10
Evidence10
Evidence
Henn
et al
. (2009)
Papadopoulou
et al
. (2009)Slide11
Evidence from ancient DNA11
EvidenceSlide12
Evidence from ancient DNA
Evidence
12
Hay
et al
. (2008)Slide13
Implications: Human migration13
Implications
Endicott
et al
. (2009)Slide14
Implications: Human migration14
Implications
Ho & Endicott (2008)Slide15
Implications: LPO hypothesis15
ImplicationsSlide16
16
LPO hypothesis
Ho et al. (2008)Slide17
CausesThe basic biological frameworkThe effects of natural selectionThe effects of calibration errorsThe effect of model misspecification
Artefacts causing time-dependent molecular rates17
CausesSlide18
Evidence18
Biological frameworkSlide19
Evidence
19
Biological frameworkSlide20
Negative selection Most mutations are deleteriousTime-dependent decline in ratio of nonsynonymous to synonymous mutationsStronger time-dependence of rates in coding DNA
20
Natural selection
Subramanian (2009)Slide21
Positive selectionSelection favouring advantageous mutationsEvidenceAdaptive mitochondrial variation in response to climatic factors
21
Natural selectionSlide22
Coalescent calibration errorGenetic divergence precedes reproductive isolation
22
Calibration errors
Reproductive
isolation
Genetic
divergenceSlide23
Fossil calibration errorFossil appearance is later than genetic divergence
23
Calibration errors
6 MyrSlide24
Phylogenetic assumptionsMitochondrial DNANo recombinationMaternally inheritedHomoplasmy
24
Model misspecificationSlide25
SaturationMutational hotspotsUnder-correction for saturation over longer time periods
25
Model misspecificationSlide26
Demographic factorsPopulation structureMisspecified demographic model
26
Model misspecification
Navascues & Emerson (2009)Slide27
Sequence errorSequencing errorPost-mortem damage(ancient DNA)Artificial mutations
Inflate rate estimatesCorrected usingphylogenetic modelsof sequence error
27
ArtefactsSlide28
Ancient DNAEvidence from ancient DNA is pivotal
28
Ancient DNASlide29
Ancient DNA
Heterochronous tipsAges up to 500,000 years
29
Ancient DNASlide30
ChallengesAncient DNA data from populationsLow variationSmall range of sampling times
Lack of control over sampling designCost of radiocarbon datingPost-mortem damage
30
Ancient DNASlide31
Concluding remarksDifficulties in estimating rates empiricallyPaucity of reliable age calibrationsRange of potential biological and methodological causes
We need to disentangle these factors so that we can estimate timescales accurately
31
Concluding remarks